Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs

Jason G. Lomnitz, Michael A. Savageau

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested. (Figure Presented).

Original languageEnglish (US)
Pages (from-to)686-701
Number of pages16
JournalACS Synthetic Biology
Volume3
Issue number9
DOIs
StatePublished - Sep 19 2014

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Phenotype
Synthetic Biology
Synthetic Genes
Circadian Clocks
Circadian Rhythm
Large scale systems
Clocks
Theoretical Models
Genes
Innovation
Genotype
Mathematical models
Networks (circuits)

Keywords

  • circuit architecture
  • dynamic phenotypes
  • mathematically controlled comparison
  • mode of transcription control
  • system design space

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Biomedical Engineering

Cite this

Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs. / Lomnitz, Jason G.; Savageau, Michael A.

In: ACS Synthetic Biology, Vol. 3, No. 9, 19.09.2014, p. 686-701.

Research output: Contribution to journalArticle

Lomnitz, Jason G. ; Savageau, Michael A. / Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs. In: ACS Synthetic Biology. 2014 ; Vol. 3, No. 9. pp. 686-701.
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